I'm having a little bit of trouble following what exactly is happening.
Are you saying that you are copying images to the clipboard, and CHS is ignoring every other image copies to the clipboard, even though all images are being copied to the clipboard by the other program? Or are you saying CHS is grabbing something, but not the right image?
Sounds like a fairly simple bug to track down if i can get my head around what's going on..
Can you try a test? Between triggers of the image copy that you are interested in, if you select some text in another program and ctrl+C to copy it to clipboard, does CHS then get every image?
And can you verify in another image program that even though CHS is ignoring every other capture -- that your megastar program is actually copying every image to the clipboard?